def plane(coords, findBounds=False): """Compute a plane given an Nx3 Numpy array. Returns a Plane whose origin is the centroid of the coords. If 'findBounds' is True, returns an additional Point (the furthest point projected into plane) and an additional floating-point number (distance from origin to that point). Tip: you generally generate the input Numpy array with numpyArrayFromAtoms() """ import numpy from numpy.linalg import eig, svd, eigh centroid = coords.mean(0) centered = coords - centroid ignore, vals, vecs = svd(centered) normal = vecs[numpy.argmin(vals)] from chimera import Point, Plane, Vector origin = Point(*centroid) plane = Plane(origin, Vector(*normal)) if findBounds: maxSqDist = None for coord in coords: projected = plane.nearest(Point(*coord)) sqDist = origin.sqdistance(projected) if maxSqDist == None or sqDist > maxSqDist: maxSqDist = sqDist furthest = projected from math import sqrt return plane, projected, sqrt(maxSqDist) return plane
def plane(coords, findBounds=False):
"""Compute a plane given an Nx3 Numpy array.
Returns a Plane whose origin is the centroid of the coords.
If 'findBounds' is True, returns an additional Point (the
furthest point projected into plane) and an additional
floating-point number (distance from origin to that point).
Tip: you generally generate the input Numpy array with
numpyArrayFromAtoms()
"""
import numpy
from numpy.linalg import eig, svd, eigh
centroid = coords.mean(0)
centered = coords - centroid
ignore, vals, vecs = svd(centered)
normal = vecs[numpy.argmin(vals)]
from chimera import Point, Plane, Vector
origin = Point(*centroid)
plane = Plane(origin, Vector(*normal))
if findBounds:
maxSqDist = None
for coord in coords:
projected = plane.nearest(Point(*coord))
sqDist = origin.sqdistance(projected)
if maxSqDist == None or sqDist > maxSqDist:
maxSqDist = sqDist
furthest = projected
from math import sqrt
return plane, projected, sqrt(maxSqDist)
return plane
def surface_center_axis(surf, center, axis, csys):
if center is None:
have_box, box = surf.bbox()
if have_box:
c = box.center()
else:
from chimera import Point
c = Point(0,0,0)
elif csys:
sixf = surf.openState.xform.inverse()
c = sixf.apply(csys.xform.apply(center))
else:
c = center
if axis is None:
from chimera import Vector
a = Vector(0,0,1)
elif csys:
sixf = surf.openState.xform.inverse()
a = sixf.apply(csys.xform.apply(axis))
else:
a = axis
return c.data(), a.data()
def surface_center_axis(surf, center, axis, csys):
if center is None:
have_box, box = surf.bbox()
if have_box:
c = box.center()
else:
from chimera import Point
c = Point(0,0,0)
elif csys:
sixf = surf.openState.xform.inverse()
c = sixf.apply(csys.xform.apply(center))
else:
c = center
if axis is None:
from chimera import Vector
a = Vector(0,0,1)
elif csys:
sixf = surf.openState.xform.inverse()
a = sixf.apply(csys.xform.apply(axis))
else:
a = axis
return c.data(), a.data()
def apply_transform(self, xf):
# Apply transform to models.
from chimera import viewer, openModels as om, Point
oslist = list(set([m.openState for m in om.list()]))
# Activate inactive models in fly mode or all models mode.
ialist = []
if self.fly_mode or self.all_models:
ialist = [
os for os in set([m.openState for m in om.list()])
if not os.active
]
for os in ialist:
os.active = True
if self.fly_mode:
m, c = om.cofrMethod, om.cofr
om.cofrMethod = om.Fixed
view = 0 # TODO: use center between eyes for stereo
e = Point(*viewer.camera.eyePos(view))
om.cofr = e # Rotate about eye position
om.applyXform(xf.inverse())
om.cofr = c # Restore center of rotation
om.cofrMethod = m
else:
om.applyXform(xf)
for os in ialist:
os.active = False
def report_correlations_with_rotation(v1, v2, aboveThreshold, axis, center,
angleRange, plot):
from chimera import Vector, Point, replyobj
# Convert axis and center to v1 local coordinates so transformation
# is still valid if user rotates entire scene.
xf = v1.openState.xform.inverse()
axis = xf.apply(Vector(*axis)).data()
center = xf.apply(Point(*center)).data()
import FitMap, Matrix
replyobj.info('Correlation between %s and %s\n' % (v1.name, v2.name) +
'Rotation\tCorrelation\n')
a0, a1, astep = angleRange
angle = a0
clist = []
from Matrix import multiply_matrices, xform_matrix, rotation_transform, chimera_xform
while angle < a1:
tf = multiply_matrices(xform_matrix(v1.openState.xform),
rotation_transform(axis, angle, center),
xform_matrix(v1.openState.xform.inverse()))
xf = chimera_xform(tf)
olap, cor = FitMap.map_overlap_and_correlation(v1, v2, aboveThreshold,
xf)
replyobj.status('angle = %.4g, correlation = %.4g\n' % (angle, cor))
replyobj.info('%.4g\t%.4g\n' % (angle, cor))
clist.append((angle, cor))
angle += astep
if plot:
angles = [a for a, c in clist]
corr = [c for a, c in clist]
plot_correlation(angles, corr, v1, v2, axis, center)
def setBondLength(bond, bondLength, movingSide="smaller side", status=None):
bond.molecule.idatmValid = False
try:
br = chimera.BondRot(bond)
except ValueError, v:
if "already used" in str(v):
if status:
status(
"Cannot change length of active"
" bond rotation\nDeactivate rotation"
" and try again",
color="red")
return
if "cycle" not in str(v):
raise
if status:
status(
"Bond involved in ring/cycle\n"
"Moved bonded atoms (only) equally",
color="blue")
mid = Point([a.coord() for a in bond.atoms])
for a in bond.atoms:
v = a.coord() - mid
v.length = bondLength / 2
a.setCoord(mid + v)
return
def _vmd_trans_angle(a, b, c, delta):
"""
Simulates VMD's `trans angle` command
"""
ZERO = Point(0, 0, 0)
xf = chimera.Xform.translation(b - ZERO)
xf.rotate(cross(a - b, b - c), delta)
xf.translate(ZERO - b)
return xf
def placeFragment(fragment, resName, model="scratch", position=None):
"""place a Fragment (see Fragment.py)
'resName' is the name of the new residue that will contain the
fragment. (It will be in the 'het' chain.)
'model' can either be a chimera.Molecule instance or a string.
If the latter, then a new model is created with the string as
its .name attribute.
'position' can either be a chimera.Point or None. If None, then
the fragment is positioned at the center of the view.
"""
if isinstance(model, basestring):
model = _newModel(model)
r = _newResidue(model, resName)
needFocus = False
if position is None:
if len(chimera.openModels.list()) == 1:
needFocus = True
xf = model.openState.xform
position = xf.inverse().apply(Point(*chimera.viewer.camera.center))
# find fragment center
x = y = z = 0.0
for element, xyz in fragment.atoms:
x += xyz[0]
y += xyz[1]
z += xyz[2]
numAtoms = len(fragment.atoms)
fragCenter = Point(x / numAtoms, y / numAtoms, z / numAtoms)
correction = position - fragCenter
from chimera.molEdit import addAtom, genAtomName
atoms = []
for element, xyz in fragment.atoms:
atoms.append(
addAtom(genAtomName(element, r), Element(element), r,
Point(*xyz) + correction))
for indices, depict in fragment.bonds:
r.molecule.newBond(atoms[indices[0]], atoms[indices[1]])
if needFocus:
chimera.runCommand("focus")
return r
def singlePos(bondee, bondLen, toward=None, away=None):
if toward:
v = toward - bondee
v.normalize()
return bondee + v * bondLen
elif away:
v = bondee - away
v.normalize()
return bondee + v * bondLen
return Point(bondee.x + bondLen, bondee.y, bondee.z)
def transform_atom_positions(atoms, tf, from_atoms = None):
if from_atoms is None:
from_atoms = atoms
import _multiscale
xyz = _multiscale.get_atom_coordinates(from_atoms, transformed = False)
from _contour import affine_transform_vertices
affine_transform_vertices(xyz, tf)
from chimera import Point
for i,a in enumerate(atoms):
a.setCoord(Point(*xyz[i]))
def mark_zero():
from VolumePath import place_marker, show_volume_path_dialog
from chimera import selection as s, Point
mlist = s.currentGraphs()
if len(mlist) == 0:
place_marker((0, 0, 0))
else:
for m in mlist:
m0 = m.openState.xform.apply(Point(0, 0, 0)).data()
place_marker(m0)
show_volume_path_dialog()
def _restoreSession(self, planeData, fromGeom=False): from SimpleSession import getColor, idLookup maxNumber = 0 for data, atomIDs in planeData.items(): number, name, cmpVal, radius, thickness, colorID, origin, normal\ = data atoms = [idLookup(a) for a in atomIDs] self._instantiatePlane(number, name, self.planeOrdinal + number, getColor(colorID), radius, thickness, self._getSourceModel(atoms), atoms, chimera.Plane(Point(*origin), Vector(*normal))) maxNumber = max(number, maxNumber) self.planeOrdinal += maxNumber
def restoreRemainder():
from SimpleSession.versions.v65 import restoreWindowSize, \
restoreOpenStates, restoreSelections, restoreFontInfo, \
restoreOpenModelsAttrs, restoreModelClip, restoreSilhouettes
curSelIds = []
savedSels = []
openModelsAttrs = {'cofrMethod': 0}
from chimera import Point
openModelsAttrs['cofr'] = Point(-2.32628, -0.573985, 3.59536)
windowSize = (1864, 872)
xformMap = {
0: (((0.24085045920787, -0.88643853394015, -0.39524395231983),
31.611106929862), (-5.2556544062118, 0.24110915283208,
5.6843595710697), True),
1: (((-0.21724896247622, -0.52207222470775, 0.82476874364376),
155.76893615651), (-1.2842808932621, 1.6062919677941,
4.0957949649428), True),
2: (((0.28162879842346, -0.039178497638975, 0.95872324746056),
66.883398971617), (-0.868129924858, -1.6236021110072,
-3.4048091153303), True)
}
fontInfo = {'face': ('Sans Serif', 'Normal', 16)}
clipPlaneInfo = {}
silhouettes = {0: True, 1: True, 2: True, 41: True}
replyobj.status("Restoring window...", blankAfter=0, secondary=True)
restoreWindowSize(windowSize)
replyobj.status("Restoring open states...", blankAfter=0, secondary=True)
restoreOpenStates(xformMap)
replyobj.status("Restoring font info...", blankAfter=0, secondary=True)
restoreFontInfo(fontInfo)
replyobj.status("Restoring selections...", blankAfter=0, secondary=True)
restoreSelections(curSelIds, savedSels)
replyobj.status("Restoring openModel attributes...",
blankAfter=0,
secondary=True)
restoreOpenModelsAttrs(openModelsAttrs)
replyobj.status("Restoring model clipping...",
blankAfter=0,
secondary=True)
restoreModelClip(clipPlaneInfo)
replyobj.status("Restoring per-model silhouettes...",
blankAfter=0,
secondary=True)
restoreSilhouettes(silhouettes)
replyobj.status("Restoring remaining extension info...",
blankAfter=0,
secondary=True)
def _restoreSession(self, axisData, fromGeom=False):
from SimpleSession import getColor, idLookup
for i, data in enumerate(axisData.keys()):
atomIDs = axisData[data]
try:
number, name, cmpVal, radius, colorID, extents, center,\
direction = data
except ValueError:
number = i + 1
name, cmpVal, radius, colorID, extents, center,\
direction = data
atoms = [idLookup(a) for a in atomIDs]
self._instantiateAxis(number, name, getColor(colorID), radius,
self._getSourceModel(atoms), atoms,
Point(*center), Vector(*direction), extents)
def parse_center_axis(center, axis, csys, cmdname):
from Commands import parseCenterArg, parse_axis
if isinstance(center, (tuple, list)):
from chimera import Point
center = Point(*center)
ccs = csys
elif center:
center, ccs = parseCenterArg(center, cmdname)
else:
ccs = None
if isinstance(axis, (tuple, list)):
from chimera import Vector
axis = Vector(*axis)
axis_point = None
acs = csys
elif axis:
axis, axis_point, acs = parse_axis(axis, cmdname)
else:
axis_point = None
acs = None
if not center and axis_point:
# Use axis point if no center specified.
center = axis_point
ccs = acs
# If no coordinate system specified use axis or center coord system.
cs = (ccs or acs)
if csys is None and cs:
csys = cs
xf = cs.xform.inverse()
if center and not ccs:
center = xf.apply(center)
if axis and not acs:
axis = xf.apply(axis)
# Convert axis and center to requested coordinate system.
if csys:
xf = csys.xform.inverse()
if center and ccs:
center = xf.apply(ccs.xform.apply(center))
if axis and acs:
axis = xf.apply(acs.xform.apply(axis))
return center, axis, csys
def addDihedralBond(a1, a2, length, angleInfo, dihedInfo):
"""Make bond between two models.
The models will be combined and the originals closed.
The new model will be opened in the same id/subid as the
non-moving model.
a1/a2 are atoms in different models.
a2 and atoms in its model will be moved to form the bond.
'length' is the bond length.
'angleInfo' is a two-tuple of sequence of three atoms and
an angle that the three atoms should form.
'dihedInfo' is like 'angleInfo', but 4 atoms.
angleInfo/dihedInfo can be None if insufficient atoms
"""
if a1.molecule == a2.molecule:
raise ValueError("Atoms to be bonded must be in different models")
# first, get the distance correct
from chimera import Xform, cross, angle, Point
dvector = a1.xformCoord() - a2.xformCoord()
dvector.length = dvector.length + length
openState = a2.molecule.openState
openState.globalXform(Xform.translation(dvector))
# then angle
if angleInfo:
atoms, angleVal = angleInfo
p1, p2, p3 = [a.xformCoord() for a in atoms]
axis = cross(p1 - p2, p2 - p3)
curAngle = angle(p1, p2, p3)
delta = angleVal - curAngle
v2 = p2 - Point(0.0, 0.0, 0.0)
trans1 = Xform.translation(v2)
v2.negate()
trans2 = Xform.translation(v2)
trans1.multiply(Xform.rotation(axis, delta))
trans1.multiply(trans2)
openState.globalXform(trans1)
def getPhiPlaneParams(acceptor, bonded1, bonded2):
ap = acceptor.xformCoord()
if bonded2:
# two principal bonds
phiPlane = [ap]
midPoint = Vector(0.0, 0.0, 0.0)
for bonded in [bonded1, bonded2]:
pt = bonded.xformCoord()
phiPlane.append(pt)
midPoint = midPoint + pt.toVector()
midPoint = midPoint / 2.0
phiBasePos = Point(midPoint.x, midPoint.y, midPoint.z)
elif bonded1:
# one principal bond
phiBasePos = bonded1.xformCoord()
grandBonded = bonded1.primaryNeighbors()
for al in acceptor.allLocations():
if al in grandBonded:
grandBonded.remove(al)
break
else:
raise ValueError("No locations of acceptor %s found"
" in bond list of %s" % (acceptor, bonded1))
if len(grandBonded) == 1:
phiPlane = [ap, bonded1.xformCoord(), grandBonded[0].xformCoord()]
elif len(grandBonded) == 2:
phiPlane = [ap]
for gb in grandBonded:
phiPlane.append(gb.xformCoord())
elif len(grandBonded) == 0:
# e.g. O2
phiPlane = None
else:
raise ConnectivityError("Wrong number of grandchild"
" atoms for phi/psi acceptor %s" %
acceptor.oslIdent())
else:
return None, None
return phiPlane, phiBasePos
def clip_model(m, axis, origin, offset, slab, thickness, flip):
if origin is None:
origin = m.clipPlane.origin.data()
if axis is None:
axis = (-m.clipPlane.normal).data()
if flip:
axis = tuple([-x for x in axis])
if offset != 0:
origin = apply_offset(origin, axis, offset)
from chimera import Plane, Point, Vector
p = Plane()
p.origin = Point(*origin)
p.normal = -Vector(*axis)
m.clipPlane = p
if not slab is None:
m.useClipThickness = slab
if not thickness is None:
m.clipThickness = thickness
m.useClipPlane = True
def clip_models(models, axis, origin, coord,
offset, stagger, flip, slab, thickness):
if origin == 'center' or origin is None:
screen_origin = center_of_models(models)
elif coord == 'screen':
screen_origin = origin
else:
screen_origin = None
for m in models:
default_plane = (tuple(m.clipPlane.normal.data()) == (0,0,0))
if origin is None and not default_plane:
o = None
elif screen_origin:
xfinv = m.openState.xform.inverse()
from chimera import Point
o = xfinv.apply(Point(*screen_origin)).data()
else:
o = origin
if axis is None:
if default_plane:
a = (0,0,1)
else:
a = None
elif coord == 'screen':
xfinv = m.openState.xform.inverse()
from chimera import Vector
a = xfinv.apply(Vector(*axis)).data()
else:
a = axis
clip_model(m, a, o, offset, slab, thickness, flip)
if not stagger is None:
offset += stagger
def placeHelium(resName, model="scratch", position=None):
"""place a new helium atom
'resName' is the name of the new residue that will contain the
helium. (It will be in the 'het' chain.)
'model' can either be a chimera.Molecule instance or a string.
If the latter, then a new model is created with the string as
its .name attribute.
'position' can either be a chimera.Point or None. If None, then
the helium is positioned at the center of the view.
"""
if isinstance(model, basestring):
model = _newModel(model)
r = _newResidue(model, resName)
if position is None:
xf = model.openState.xform
position = xf.inverse().apply(Point(*chimera.viewer.camera.center))
from chimera.molEdit import addAtom
return addAtom('He1', Element('He'), r, position)
def bestLine(coords, weights=None):
import numpy
from numpy.linalg import eig, svd, eigh
if weights != None:
n = len(coords)
matWeights = weights.reshape((n, 1))
wcoords = matWeights * coords
wsum = weights.sum()
centroid = wcoords.sum(0) / wsum
centered = coords - centroid
# Tom Goddard's method too subtle for me!
#v33 = numpy.dot(coords.transpose(), wcoords) / wsum \
# - numpy.outer(centroid, centroid)
#vals, vecs = eigh(v33)
ignore, vals, vecs = svd(matWeights * centered)
else:
centroid = coords.mean(0)
centered = coords - centroid
ignore, vals, vecs = svd(centered)
normLineVec = vecs[numpy.argmax(vals)]
from chimera import Point, Vector
return Point(*centroid), Vector(*normLineVec), centroid, normLineVec, \
centered, vals, vecs
def anglePos(atomPos, bondPos, bondLength, degrees, coplanar=None):
if coplanar:
# may have one or two coplanar positions specified,
# if two, compute both resultant positions and average
# (the up vector has to be negated for the second one)
xforms = []
if len(coplanar) > 2:
raise ValueError, \
"More than 2 coplanar positions specified!"
for cpos in coplanar:
up = cpos - atomPos
if xforms:
up.negate()
xform = Xform.lookAt(atomPos, bondPos, up)
# lookAt puts ref point opposite that of zAlign, so
# rotate 180 degrees around y axis
xform.premultiply(Xform.yRotation(180))
xforms.append(xform)
else:
xforms = [Xform.zAlign(atomPos, bondPos)]
points = []
for xform in xforms:
radians = pi * degrees / 180.0
angle = Point(0.0, bondLength * sin(radians),
bondLength * cos(radians))
xform.invert()
points.append(xform.apply(angle))
if len(points) > 1:
midpoint = points[0] + (points[1] - points[0]) / 2.0
v = midpoint - atomPos
v.length = bondLength
return atomPos + v
return points[0]
def findPt(n1, n2, n3, dist, angle, dihed):
# cribbed from Midas addgrp command
v12 = n2 - n1
v13 = n3 - n1
v12.normalize()
x = cross(v13, v12)
x.normalize()
y = cross(v12, x)
y.normalize()
mat = [0.0] * 12
for i in range(3):
mat[i * 4] = x[i]
mat[1 + i * 4] = y[i]
mat[2 + i * 4] = v12[i]
mat[3 + i * 4] = n1[i]
xform = Xform.xform(*mat)
radAngle = pi * angle / 180.0
tmp = dist * sin(radAngle)
radDihed = pi * dihed / 180.0
pt = Point(tmp * sin(radDihed), tmp * cos(radDihed), dist * cos(radAngle))
return xform.apply(pt)
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
openModelsArgs = {}
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m], baseId=ids[0] + modelOffset, subid=ids[1])
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
for mid, name, chain, pos, insert, rcid, lcid, ss, ribbonDrawMode, \
ribbonDisplay, label in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
resInfo['position'],
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label'])
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, surfaceDisplay, surfaceCategory, surfaceOpacity, radius, vdw, \
bfactor, occupancy, charge, idatmType in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['bfactor']),
expandSummary(atomInfo['occupancy']),
expandSummary(atomInfo['charge']),
expandSummary(atomInfo['idatmType'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if bfactor is not None:
a.bfactor = bfactor
if occupancy is not None:
a.occupancy = occupancy
if charge is not None:
a.charge = charge
if idatmType:
a.idatmType = idatmType
for atoms, drawMode, display in zip(bondInfo['atoms'],
expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display'])):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(
Point(*tuple([float(c) for c in crdString.split()])),
coordSet)
if key == active:
m.activeCoordSet = coordSet
def axis(coords,
findBounds=False,
findRadius=False,
iterate=True,
weights=None):
"""Compute an axis given an Nx3 Numpy array.
Returns a Point (centroid) and a Vector (unit direction vector).
If 'findBounds' is True, returns two additional floating point
values -- the scaling factors for the vector to reach the
approximate bounds of the axis defined by the array values.
If 'findRadius' is True, returns yet another floating-point
value: the average coord-axis distance.
'weights' is a numpy array used to weight the 'coords'; typicaly used
for mass weighting.
Tip: you generally generate the input Numpy array with
numpyArrayFromAtoms()
"""
if weights != None and iterate:
raise ValueError("'iterate' does not consider 'weights'")
import numpy
from chimera import Point, Vector
def reshapeTo(source, target):
scalings = numpy.repeat(source, 3)
scalings.shape = len(target), 3
return scalings
pt, longVec, centroid, normLineVec, centered, vals, vecs = bestLine(
coords, weights=weights)
# for short helices, best axis not necessarily longest
normLineVec = vecs[numpy.argmin([axisEval(v, centered) for v in vecs])]
vec = Vector(*normLineVec)
best = None
while iterate:
# nearest point on line
ts = numpy.tensordot(normLineVec, centered, (0, 1)) \
/ numpy.dot(normLineVec, normLineVec)
linePts = numpy.outer(ts, normLineVec)
# distance
temp = (centered - linePts)
dists = numpy.sqrt((temp * temp).sum(-1))
avgDist = dists.mean(0)
diffs = dists - avgDist
val = (diffs * diffs).sum()
if best == None or val < best:
best = val
oldPt = pt
oldVec = vec
oldCentered = centered
oldLineVec = normLineVec
else:
pt = oldPt
vec = oldVec
centered = oldCentered
normLineVec = oldLineVec
break
# find the point that is 1/3 from the current distance to
# the average distance and correct line and centroid based
# on that point
nonzero = dists > 0.0001
if not len(nonzero):
break
nzCentered = centered.compress(nonzero, 0)
nzLinePts = linePts.compress(nonzero, 0)
nzDists = dists.compress(nonzero, 0)
correctionTargets = linePts + (nzCentered - linePts) * reshapeTo(
(2 + avgDist / nzDists) / 3.0, nzCentered)
# centroid motion
#centroid += (correctionTargets - nzLinePts).mean(0)
# vector correction
corrVecs = correctionTargets
dots = (corrVecs * normLineVec).sum(1)
corrVecs[dots < 0] *= -1
normLineVec = corrVecs.mean(0)
normLineVec /= numpy.sqrt((normLineVec * normLineVec).sum())
centered = coords - centroid
pt = Point(*centroid)
vec = Vector(*normLineVec)
retVals = (pt, vec)
if findBounds:
dotted = numpy.dot(centered, normLineVec)
retVals += (dotted.min(), dotted.max())
if findRadius:
dists = axisDists(normLineVec, centered)
retVals += (dists.mean(0), )
return retVals
def Apply(self):
savePaths = self.getPaths()
if not savePaths:
replyobj.error("No save file specified\n")
return
from OpenSave import osOpen
saveFile = osOpen(savePaths[0], "w")
mols = chimera.openModels.list(modelTypes=[chimera.Molecule])
for mol in mols:
print>>saveFile, "Model %s is %s" % (mol.oslIdent(),
mol.name)
sm = self.structMeasure
selected = self.saveTypes.getcurselection()
if DISTANCES in selected:
print>>saveFile, "\nDistance information"
output = {}
for d in sm.distances:
a1, a2 = d.atoms
distID = d.id
if d.distance[-1].isdigit():
dval = d.distance
else:
# omit angstrom character
dval = d.distance[:-1]
output[distID] = "%2d %s <-> %s: %s" % (
distID, sm.atomLabel(a1),
sm.atomLabel(a2), dval)
ids = output.keys()
ids.sort()
for distID in ids:
print>>saveFile, output[distID]
if ANGLES in selected:
print>>saveFile, "\nAngles/Torsions"
printables = []
maxLabel = 0
for atoms in sm.angleInfo:
labelArgs = tuple([sm.atomLabel(a)
for a in atoms])
if len(atoms) == 3:
label = "%s -> %s -> %s" % labelArgs
func = chimera.angle
else:
label = "%s -> %s -> %s -> %s" \
% labelArgs
func = chimera.dihedral
maxLabel = max(maxLabel, len(label))
printables.append((label, "%8.3f" %
func(*tuple([a.xformCoord()
for a in atoms]))))
format = "%%%ds: %%s" % maxLabel
for printArgs in printables:
print>>saveFile, format % printArgs
if BONDROTS in selected:
print>>saveFile, "\nBond rotations"
printables = []
maxLabel = 0
for br in sm.rotations:
na, fa = sm.dihedEndAtoms(br)
label = "%s -> %s -> %s -> %s" % (
sm.atomLabel(na),
sm.atomLabel(br.atoms[0]),
sm.atomLabel(br.atoms[1]),
sm.atomLabel(fa))
maxLabel = max(maxLabel, len(label))
printables.append((label,
"%8.3f" % sm.dihedral(br),
"%8.3f" % br.get()))
format = "%%%ds: %%s (delta: %%s)" % maxLabel
for printArgs in printables:
print>>saveFile, format % printArgs
if GEOMETRIES in selected:
print>>saveFile, "\nAxes"
print>>saveFile, "axis name, length, center, direction"
from Axes import axisManager
axes = axisManager.axes
axes.sort(lambda a1, a2: cmp(a1.name, a2.name))
nameSize = max([0] + [len(a.name) for a in axes])
from chimera import Point
for axis in axes:
ends = [axis.direction * ext + axis.center
for ext in axis.extents]
cx, cy, cz = Point(ends)
dx, dy, dz = axis.direction
print>>saveFile, "%*s: %6.3f (%7.3f, %7.3f," \
" %7.3f) (%6.3f, %6.3f, %6.3f)" % (
nameSize, axis.name,
abs(axis.extents[0] - axis.extents[1]),
cx, cy, cz, dx, dy, dz)
print>>saveFile, "\nPlanes"
print>>saveFile, "plane name, center, normal, radius"
from Planes import planeManager
planes = planeManager.planes
planes.sort(lambda p1, p2: cmp(p1.name, p2.name))
nameSize = max([0] + [len(pl.name) for pl in planes])
for plane in planes:
ox, oy, oz = plane.plane.origin
nx, ny, nz = plane.plane.normal
print>>saveFile, "%*s: (%7.3f, %7.3f, %7.3f)" \
" (%6.3f, %6.3f, %6.3f) %.3f" % (nameSize, plane.name,
ox, oy, oz, nx, ny, nz, plane.radius)
saveFile.close()
def xform_xyz(xyz, from_xform=None, to_xform=None):
from chimera import Point
p = Point(*tuple(xyz))
p1 = from_xform.apply(p) if from_xform else p
p2 = to_xform.inverse().apply(p1) if to_xform else p1
return (p2.x, p2.y, p2.z)
from chimera import runCommand
from chimera import openModels, Molecule
from os import chdir, listdir
import chimera
from WriteMol2 import writeMol2
import sys
file = open("com.txt")
for line in file:
if line.find("centroid has center") != -1:
#print "OPENED:%s" % line
word = line.split()
#print word
x = float(word[3])
y = float(word[4])
z = float(word[5]) + 16
center = Point(x, y, z)
runCommand("open " + sys.argv[1])
model0 = openModels.list(id=0, modelTypes=[Molecule])[0]
c = BuildStructure.placeHelium('com', model=model0, position=center)
runCommand("select He")
runCommand("namesel helium")
runCommand("select helium za>10")
runCommand("del sel")
runCommand("del helium")
writeMol2(chimera.openModels.list(modelTypes=[chimera.Molecule]), sys.argv[1][:-4] + ".mol2")
runCommand("close all")
def placePeptide(sequence,
phiPsis,
model="scratch",
position=None,
rotlib=None,
chainID='A'):
"""place a peptide sequence
'sequence' contains the (upper case) sequence
'phiPsis' is a list of phi/psi tuples, one per residue
'model' can either be a chimera.Molecule instance or a string.
If the latter, then a new model is created with the string as
its .name attribute.
'position' can either be a chimera.Point or None. If None, then
the fragment is positioned at the center of the view.
"""
if not sequence:
raise ValueError("No sequence supplied")
sequence = sequence.upper()
if not sequence.isupper():
raise ValueError("Sequence contains non-alphabetic characters")
from chimera.resCode import protein1to3
for c in sequence:
if c not in protein1to3:
raise ValueError("Unrecognized protein 1-letter code:" " %s" % c)
if len(sequence) != len(phiPsis):
raise ValueError("Number of phi/psis not equal to" " sequence length")
if isinstance(model, basestring):
model = _newModel(model)
needFocus = False
if position is None:
if len(chimera.openModels.list()) == 1:
needFocus = True
xf = model.openState.xform
position = xf.inverse().apply(Point(*chimera.viewer.camera.center))
prev = [None] * 3
pos = 1
from Midas.addAA import DIST_N_C, DIST_CA_N, DIST_C_CA, DIST_C_O
from chimera.molEdit import findPt, addAtom, addDihedralAtom
serialNumber = None
residues = []
for c, phiPsi in zip(sequence, phiPsis):
phi, psi = phiPsi
while model.findResidue(chimera.MolResId(chainID, pos)):
pos += 1
r = model.newResidue(protein1to3[c], chainID, pos, ' ')
residues.append(r)
for backbone, dist, angle, dihed in (('N', DIST_N_C, 116.6, psi),
('CA', DIST_CA_N, 121.9, 180.0),
('C', DIST_C_CA, 110.1, phi)):
if prev[0] == None:
pt = Point(0.0, 0.0, 0.0)
elif prev[1] == None:
pt = Point(dist, 0.0, 0.0)
elif prev[2] == None:
pt = findPt(prev[0].coord(), prev[1].coord(),
Point(0.0, 1.0, 0.0), dist, angle, 0.0)
else:
pt = findPt(prev[0].coord(), prev[1].coord(), prev[2].coord(),
dist, angle, dihed)
a = addAtom(backbone,
Element(backbone[0]),
r,
pt,
serialNumber=serialNumber,
bondedTo=prev[0])
serialNumber = a.serialNumber + 1
prev = [a] + prev[:2]
o = addDihedralAtom("O",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
120.4,
180.0 + psi,
bonded=True)
# C terminus O/OXT at different angle than mainchain O
model.deleteAtom(o)
addDihedralAtom("O",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
117.0,
180.0 + psi,
bonded=True)
addDihedralAtom("OXT",
Element("O"),
prev[0],
prev[1],
prev[2],
DIST_C_O,
117.0,
psi,
bonded=True)
from Rotamers import useBestRotamers
# have to process one by one, otherwise side-chain clashes will occur
kw = {}
if rotlib:
kw['lib'] = rotlib
for r in residues:
useBestRotamers("same", [r], criteria="cp", log=False, **kw)
# find peptide center
coords = []
for r in residues:
coords.extend([a.coord() for a in r.atoms])
center = Point(coords)
correction = position - center
for r in residues:
for a in r.atoms:
a.setCoord(a.coord() + correction)
from Midas import ksdssp
ksdssp([model])
if needFocus:
chimera.runCommand("focus")
return residues
def restoreMolecules(molInfo, resInfo, atomInfo, bondInfo, crdInfo):
from SimpleSession import registerAttribute
items = []
sm = globals.sessionMap
res2mol = []
atom2mol = []
for ids, name, cid, display, lineWidth, pointSize, stickScale, \
pdbHeaders, surfaceOpacity, ballScale, vdwDensity, autochain, \
ribbonHidesMainchain, riCID, aromaticCID, aromaticDisplay, \
aromaticLineType, aromaticMode, hidden in zip(
expandSummary(molInfo['ids']),
expandSummary(molInfo['name']),
expandSummary(molInfo['color']),
expandSummary(molInfo['display']),
expandSummary(molInfo['lineWidth']),
expandSummary(molInfo['pointSize']),
expandSummary(molInfo['stickScale']),
molInfo['pdbHeaders'],
expandSummary(molInfo['surfaceOpacity']),
expandSummary(molInfo['ballScale']),
expandSummary(molInfo['vdwDensity']),
expandSummary(molInfo['autochain']),
expandSummary(molInfo['ribbonHidesMainchain']),
expandSummary(molInfo['ribbonInsideColor']),
expandSummary(molInfo['aromaticColor']),
expandSummary(molInfo['aromaticDisplay']),
expandSummary(molInfo['aromaticLineType']),
expandSummary(molInfo['aromaticMode']),
expandSummary(molInfo['hidden'])
):
m = chimera.Molecule()
sm[len(items)] = m
items.append(m)
m.name = name
from SimpleSession import modelMap, modelOffset
chimera.openModels.add([m],
baseId=ids[0] + modelOffset,
subid=ids[1],
hidden=hidden)
modelMap.setdefault(ids, []).append(m)
m.color = getColor(cid)
m.display = display
m.lineWidth = lineWidth
m.pointSize = pointSize
m.stickScale = stickScale
m.setAllPDBHeaders(pdbHeaders)
m.surfaceOpacity = surfaceOpacity
m.ballScale = ballScale
m.vdwDensity = vdwDensity
m.autochain = autochain
m.ribbonHidesMainchain = ribbonHidesMainchain
m.ribbonInsideColor = getColor(riCID)
m.aromaticColor = getColor(aromaticCID)
m.aromaticDisplay = aromaticDisplay
m.aromaticLineType = aromaticLineType
m.aromaticMode = aromaticMode
if molInfo['optional']:
for attrName, info in molInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Molecule, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for m, val in zip(items, vals):
if val is not None:
setattr(m, attrName, val)
resStart = len(items)
for mid, name, chain, pos, insert, rcid, lcid, ss, ssId, ribbonDrawMode, \
ribbonDisplay, label, labelOffset, isHet, fillDisplay, fillMode in zip(
expandSummary(resInfo['molecule']),
expandSummary(resInfo['name']),
expandSummary(resInfo['chain']),
expandSequentialSummary(resInfo['position']),
expandSummary(resInfo['insert']),
expandSummary(resInfo['ribbonColor']),
expandSummary(resInfo['labelColor']),
expandSummary(resInfo['ss']),
expandSummary(resInfo['ssId']),
expandSummary(resInfo['ribbonDrawMode']),
expandSummary(resInfo['ribbonDisplay']),
expandSummary(resInfo['label']),
expandSummary(resInfo['labelOffset']),
expandSummary(resInfo['isHet']),
expandSummary(resInfo['fillDisplay']),
expandSummary(resInfo['fillMode']),
):
m = idLookup(mid)
r = m.newResidue(name, chain, pos, insert)
sm[len(items)] = r
items.append(r)
r.ribbonColor = getColor(rcid)
r.labelColor = getColor(lcid)
r.isHelix, r.isStrand, r.isTurn = ss
r.ssId = ssId
r.ribbonDrawMode = ribbonDrawMode
r.ribbonDisplay = ribbonDisplay
r.label = label
if labelOffset is not None:
r.labelOffset = labelOffset
r.isHet = isHet
r.fillDisplay = fillDisplay
r.fillMode = fillMode
if resInfo['optional']:
residues = items[resStart:]
for attrName, info in resInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Residue, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for r, val in zip(residues, vals):
if val is not None:
setattr(r, attrName, val)
atomStart = len(items)
for rid, name, element, cid, vcid, lcid, scid, drawMode, display, \
label, labelOffet, surfaceDisplay, surfaceCategory, surfaceOpacity, \
radius, vdw, idatmType, altLoc in zip(
expandSummary(atomInfo['residue']),
expandSummary(atomInfo['name']),
expandSummary(atomInfo['element']),
expandSummary(atomInfo['color']),
expandSummary(atomInfo['vdwColor']),
expandSummary(atomInfo['labelColor']),
expandSummary(atomInfo['surfaceColor']),
expandSummary(atomInfo['drawMode']),
expandSummary(atomInfo['display']),
expandSummary(atomInfo['label']),
expandSummary(atomInfo['labelOffset']),
expandSummary(atomInfo['surfaceDisplay']),
expandSummary(atomInfo['surfaceCategory']),
expandSummary(atomInfo['surfaceOpacity']),
expandSummary(atomInfo['radius']),
expandSummary(atomInfo['vdw']),
expandSummary(atomInfo['idatmType']),
expandSummary(atomInfo['altLoc'])
):
r = idLookup(rid)
a = r.molecule.newAtom(name, chimera.Element(element))
sm[len(items)] = a
items.append(a)
r.addAtom(a)
a.color = getColor(cid)
a.vdwColor = getColor(vcid)
a.labelColor = getColor(lcid)
a.surfaceColor = getColor(scid)
a.drawMode = drawMode
a.display = display
a.label = label
if labelOffset is not None:
a.labelOffset = labelOffset
a.surfaceDisplay = surfaceDisplay
a.surfaceCategory = surfaceCategory
a.surfaceOpacity = surfaceOpacity
a.radius = radius
a.vdw = vdw
if idatmType:
a.idatmType = idatmType
a.altLoc = altLoc
if atomInfo['optional']:
atoms = items[atomStart:]
for attrName, info in atomInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Atom, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for a, val in zip(atoms, vals):
if val is not None:
setattr(a, attrName, val)
bondStart = len(items)
for atoms, drawMode, display, label, labelOffset, radius in zip(
bondInfo['atoms'], expandSummary(bondInfo['drawMode']),
expandSummary(bondInfo['display']),
expandSummary(bondInfo['label']),
expandSummary(bondInfo['labelOffset']),
expandSummary(bondInfo['radius'])):
a1, a2 = [idLookup(a) for a in atoms]
b = a1.molecule.newBond(a1, a2)
sm[len(items)] = b
items.append(b)
b.drawMode = drawMode
b.display = display
b.label = label
if labelOffset is not None:
b.labelOffset = labelOffset
b.radius = radius
if bondInfo.get('optional', {}):
bonds = items[bondStart:]
for attrName, info in bondInfo['optional'].items():
hashable, sv = info
registerAttribute(chimera.Bond, attrName, hashable=hashable)
vals = expandSummary(sv, hashable=hashable)
for b, val in zip(bonds, vals):
if val is not None:
setattr(b, attrName, val)
from chimera import Point
for mid, crdSets in crdInfo.items():
m = idLookup(mid)
active = crdSets.pop('active')
for key, crds in crdSets.items():
coordSet = m.newCoordSet(key, len(crds))
for aid, crdString in crds:
idLookup(aid).setCoord(
Point(*tuple([float(c) for c in crdString.split()])),
coordSet)
if key == active:
m.activeCoordSet = coordSet
def restoreRemainder():
from SimpleSession.versions.v65 import restoreWindowSize, \
restoreOpenStates, restoreSelections, restoreFontInfo, \
restoreOpenModelsAttrs, restoreModelClip, restoreSilhouettes
curSelIds = []
savedSels = []
openModelsAttrs = {'cofrMethod': 0}
from chimera import Point
openModelsAttrs['cofr'] = Point(54.1036, 9.4266, 4.26939)
windowSize = (904, 945)
xformMap = {
0: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True),
1: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True),
2: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True),
3: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True),
4: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True),
5: (((-0.30580948052178, 0.30245992253846, 0.90277270499336),
116.52999621315), (75.916893346571, -22.475613343026,
33.625921716357), True)
}
fontInfo = {'face': (u'Fixed', u'Bold', 24)}
clipPlaneInfo = {}
silhouettes = {
0: True,
1: True,
2: True,
3: True,
4: True,
5: True,
374: True
}
replyobj.status("Restoring window...", blankAfter=0, secondary=True)
restoreWindowSize(windowSize)
replyobj.status("Restoring open states...", blankAfter=0, secondary=True)
restoreOpenStates(xformMap)
replyobj.status("Restoring font info...", blankAfter=0, secondary=True)
restoreFontInfo(fontInfo)
replyobj.status("Restoring selections...", blankAfter=0, secondary=True)
restoreSelections(curSelIds, savedSels)
replyobj.status("Restoring openModel attributes...",
blankAfter=0,
secondary=True)
restoreOpenModelsAttrs(openModelsAttrs)
replyobj.status("Restoring model clipping...",
blankAfter=0,
secondary=True)
restoreModelClip(clipPlaneInfo)
replyobj.status("Restoring per-model silhouettes...",
blankAfter=0,
secondary=True)
restoreSilhouettes(silhouettes)
replyobj.status("Restoring remaining extension info...",
blankAfter=0,
secondary=True)